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/*
* geometry.c
*
* Geometry of diffraction
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <gsl/gsl_poly.h>
#include <assert.h>
#include "utils.h"
#include "cell.h"
#include "image.h"
#include "peaks.h"
#include "beam-parameters.h"
#define MAX_CPEAKS (256 * 256)
static signed int locate_peak(double x, double y, double z, double k,
struct detector *det, double *xdap, double *ydap)
{
int p;
signed int found = -1;
const double den = k + z;
for ( p=0; p<det->n_panels; p++ ) {
double xd, yd, cl;
double xda, yda;
/* Camera length for this panel */
cl = det->panels[p].clen;
/* Coordinates of peak relative to central beam, in m */
xd = cl * x / den;
yd = cl * y / den;
/* Convert to pixels */
xd *= det->panels[p].res;
yd *= det->panels[p].res;
/* Add the coordinates of the central beam */
xda = xd + det->panels[p].cx;
yda = yd + det->panels[p].cy;
/* Now, is this on this panel? */
if ( xda < det->panels[p].min_x ) continue;
if ( xda > det->panels[p].max_x ) continue;
if ( yda < det->panels[p].min_y ) continue;
if ( yda > det->panels[p].max_y ) continue;
/* If peak appears on multiple panels, reject it */
if ( found != -1 ) return -1;
/* Woohoo! */
found = p;
*xdap = xda;
*ydap = yda;
}
return found;
}
static double excitation_error(double xl, double yl, double zl,
double ds, double k)
{
double tt, al;
double r;
tt = angle_between(0.0, 0.0, 1.0, xl, yl, zl+k);
al = M_PI_2 - asin(-zl/ds);
r = ( ds * sin(al) / sin(tt) ) - k;
return r;
}
struct cpeak *find_intersections(struct image *image, UnitCell *cell,
int *n, int output)
{
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
struct cpeak *cpeaks;
int np = 0;
int hmax, kmax, lmax;
double mres;
signed int h, k, l;
double bandwidth = image->bw;
double divergence = image->div;
double lambda = image->lambda;
const double profile_cutoff = 0.005e9; /* 0.1 nm^-1 */
double klow, kcen, khigh; /* Wavenumber */
cpeaks = malloc(sizeof(struct cpeak)*MAX_CPEAKS);
if ( cpeaks == NULL ) {
*n = 0;
return NULL;
}
cell_get_reciprocal(cell, &asx, &asy, &asz,
&bsx, &bsy, &bsz,
&csx, &csy, &csz);
mres = 1.0 / 8.0e-10; /* 8 Angstroms */
hmax = mres / modulus(asx, asy, asz);
kmax = mres / modulus(bsx, bsy, bsz);
lmax = mres / modulus(csx, csy, csz);
/* "low" gives the largest Ewald sphere,
* "high" gives the smallest Ewald sphere. */
klow = 1.0/(lambda - lambda*bandwidth/2.0);
kcen = 1.0/lambda;
khigh = 1.0/(lambda + lambda*bandwidth/2.0);
for ( h=-hmax; h<hmax; h++ ) {
for ( k=-kmax; k<kmax; k++ ) {
for ( l=-lmax; l<lmax; l++ ) {
double xl, yl, zl;
double ds, ds_sq;
double rlow, rhigh; /* "Excitation error" */
signed int p; /* Panel number */
double xda, yda; /* Position on detector */
int close, inside;
/* Ignore central beam */
if ( (h==0) && (k==0) && (l==0) ) continue;
/* Get the coordinates of the reciprocal lattice point */
zl = h*asz + k*bsz + l*csz;
/* Throw out if it's "in front" */
if ( zl > profile_cutoff ) continue;
xl = h*asx + k*bsx + l*csx;
yl = h*asy + k*bsy + l*csy;
/* Calculate reciprocal lattice point modulus (and square) */
ds_sq = modulus_squared(xl, yl, zl); /* d*^2 */
ds = sqrt(ds_sq);
if ( ds > mres ) continue; /* Outside resolution range */
/* Calculate excitation errors */
rlow = excitation_error(xl, yl, zl, ds, klow);
rhigh = excitation_error(xl, yl, zl, ds, khigh);
/* Is the reciprocal lattice point close to either extreme of
* the sphere, maybe just outside the "Ewald volume"? */
close = (fabs(rlow) < profile_cutoff)
|| (fabs(rhigh) < profile_cutoff);
/* Is the reciprocal lattice point somewhere between the
* extremes of the sphere, i.e. inside the "Ewald volume"? */
inside = signbit(rlow) ^ signbit(rhigh);
/* Can't be both inside and close */
if ( inside ) close = 0;
/* Neither? Skip it. */
if ( !(close || inside) ) continue;
/* If the "lower" Ewald sphere is a long way away, use the
* position at which the Ewald sphere would just touch the
* reflection. */
if ( rlow > profile_cutoff ) rlow = profile_cutoff;
if ( rlow < -profile_cutoff ) rlow = -profile_cutoff;
/* As above, other side. */
if ( rhigh > profile_cutoff ) rhigh = profile_cutoff;
if ( rhigh < -profile_cutoff ) rhigh = -profile_cutoff;
/* Locate peak on detector. */
p = locate_peak(xl, yl, zl, kcen, image->det, &xda, &yda);
if ( p == -1 ) continue;
cpeaks[np].h = h;
cpeaks[np].k = k;
cpeaks[np].l = l;
cpeaks[np].x = xda;
cpeaks[np].y = yda;
np++;
if ( output ) {
printf("%3i %3i %3i %6f (at %5.2f,%5.2f) %9e %9e\n",
h, k, l, 0.0, xda, yda, rlow, rhigh);
}
if ( np == MAX_CPEAKS ) goto out;
}
}
}
out:
*n = np;
return cpeaks;
}
double integrate_all(struct image *image, struct cpeak *cpeaks, int n)
{
double itot = 0.0;
int i;
for ( i=0; i<n; i++ ) {
float x, y, intensity;
if ( integrate_peak(image, cpeaks[i].x, cpeaks[i].y, &x, &y,
&intensity, NULL, NULL, 0, 0) ) continue;
itot += intensity;
}
return itot;
}
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